[Genabel-commits] r848 - pkg/ProbABEL/examples

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2012-03-17 15:16:58 +0100 (Sat, 17 Mar 2012)
New Revision: 848

Modified:
   pkg/ProbABEL/examples/example_all.sh
   pkg/ProbABEL/examples/example_bt.sh
   pkg/ProbABEL/examples/example_cox.sh
   pkg/ProbABEL/examples/example_mms.sh
   pkg/ProbABEL/examples/example_qt.sh
Log:
Reformatted the ProbABEL example test scripts so they are more readable.

Modified: pkg/ProbABEL/examples/example_all.sh
===================================================================
--- pkg/ProbABEL/examples/example_all.sh	2012-03-04 20:31:40 UTC (rev 847)
+++ pkg/ProbABEL/examples/example_all.sh	2012-03-17 14:16:58 UTC (rev 848)
@@ -1,5 +1,3 @@
-
-
 echo "extracting IDS..."
 perl ../bin/extIDS.pl < test.mldose > mldose.IDS
 
@@ -10,4 +8,3 @@
 sh example_bt.sh
 sh example_cox.sh
 sh example_mms.sh
-

Modified: pkg/ProbABEL/examples/example_bt.sh
===================================================================
--- pkg/ProbABEL/examples/example_bt.sh	2012-03-04 20:31:40 UTC (rev 847)
+++ pkg/ProbABEL/examples/example_bt.sh	2012-03-17 14:16:58 UTC (rev 848)
@@ -3,7 +3,20 @@
     srcdir="."
 fi
 
-../src/palogist -p ${srcdir}/logist_data.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o logist
-../src/palogist -p ${srcdir}/logist_data.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o logist_fv
+../src/palogist \
+    -p ${srcdir}/logist_data.txt \
+    -d ${srcdir}/test.mldose \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 \
+    -o logist
 
+../src/palogist \
+    -p ${srcdir}/logist_data.txt \
+    -d ${srcdir}/test.dose.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 \
+    -o logist_fv
+
 diff logist_add.out.txt logist_fv_add.out.txt

Modified: pkg/ProbABEL/examples/example_cox.sh
===================================================================
--- pkg/ProbABEL/examples/example_cox.sh	2012-03-04 20:31:40 UTC (rev 847)
+++ pkg/ProbABEL/examples/example_cox.sh	2012-03-17 14:16:58 UTC (rev 848)
@@ -3,7 +3,19 @@
     srcdir="."
 fi
 
-../src/pacoxph -p ${srcdir}/coxph_data.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o coxph
-../src/pacoxph -p ${srcdir}/coxph_data.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o coxph_fv
+../src/pacoxph \
+    -p ${srcdir}/coxph_data.txt \
+    -d ${srcdir}/test.mldose \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 \
+    -o coxph
+../src/pacoxph \
+    -p ${srcdir}/coxph_data.txt \
+    -d ${srcdir}/test.dose.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 \
+    -o coxph_fv
 
 diff coxph_add.out.txt coxph_fv_add.out.txt

Modified: pkg/ProbABEL/examples/example_mms.sh
===================================================================
--- pkg/ProbABEL/examples/example_mms.sh	2012-03-04 20:31:40 UTC (rev 847)
+++ pkg/ProbABEL/examples/example_mms.sh	2012-03-17 14:16:58 UTC (rev 848)
@@ -3,13 +3,35 @@
     srcdir="."
 fi
 
-../src/palinear -p ${srcdir}/mmscore_pheno.PHE  -i ${srcdir}/mmscore_gen.mlinfo -d ${srcdir}/mmscore_gen.mldose --sep="," -o mmscore --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
-../src/palinear -p ${srcdir}/mmscore_pheno.PHE  -i ${srcdir}/mmscore_gen.mlinfo -d ${srcdir}/mmscore_gen.dose.fvi --sep="," -o mmscore_fv  --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
+../src/palinear \
+    -p ${srcdir}/mmscore_pheno.PHE \
+    -i ${srcdir}/mmscore_gen.mlinfo \
+    -d ${srcdir}/mmscore_gen.mldose \
+    --sep="," -o mmscore \
+    --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
 
+../src/palinear \
+    -p ${srcdir}/mmscore_pheno.PHE \
+    -i ${srcdir}/mmscore_gen.mlinfo \
+    -d ${srcdir}/mmscore_gen.dose.fvi \
+    --sep="," -o mmscore_fv \
+    --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
+
 diff mmscore_add.out.txt mmscore_fv_add.out.txt
 
 
-../src/palinear -p ${srcdir}/mmscore_pheno.PHE  -i ${srcdir}/mmscore_gen.mlinfo -d ${srcdir}/mmscore_gen.mlprob --ngpreds=2 --sep="," -o mmscore_prob --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
-../src/palinear -p ${srcdir}/mmscore_pheno.PHE  -i ${srcdir}/mmscore_gen.mlinfo -d ${srcdir}/mmscore_gen.prob.fvi --ngpreds=2 --sep="," -o mmscore_prob_fv  --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
+../src/palinear \
+    -p ${srcdir}/mmscore_pheno.PHE \
+    -i ${srcdir}/mmscore_gen.mlinfo \
+    -d ${srcdir}/mmscore_gen.mlprob \
+    --ngpreds=2 --sep="," -o mmscore_prob \
+    --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
 
+../src/palinear \
+    -p ${srcdir}/mmscore_pheno.PHE \
+    -i ${srcdir}/mmscore_gen.mlinfo \
+    -d ${srcdir}/mmscore_gen.prob.fvi \
+    --ngpreds=2 --sep="," -o mmscore_prob_fv \
+    --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
+
 diff mmscore_prob_add.out.txt mmscore_prob_fv_add.out.txt

Modified: pkg/ProbABEL/examples/example_qt.sh
===================================================================
--- pkg/ProbABEL/examples/example_qt.sh	2012-03-04 20:31:40 UTC (rev 847)
+++ pkg/ProbABEL/examples/example_qt.sh	2012-03-17 14:16:58 UTC (rev 848)
@@ -4,38 +4,115 @@
 fi
 
 echo "base analysis"
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o height_base
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o height_base_fv
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.mldose \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 \
+    -o height_base
 
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.dose.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 \
+    -o height_base_fv
+
 diff height_base_add.out.txt height_base_fv_add.out.txt
 
+
 echo "Option --allcov"
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --allcov -o height_allcov
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --allcov -o height_allcov_fv
+../src/palinear -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.mldose \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --allcov \
+    -o height_allcov
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.dose.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --allcov \
+    -o height_allcov_fv
 
 diff height_allcov_add.out.txt height_allcov_fv_add.out.txt
 
+
 echo "Option --interaction=1"
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --interaction=1 -o height_int1
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --interaction=1 -o height_int1_fv
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.mldose \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --interaction=1 \
+    -o height_int1
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.dose.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --interaction=1 \
+    -o height_int1_fv
 
 diff height_int1_add.out.txt height_int1_fv_add.out.txt
 
+
 echo "Option --robust"
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --robust -o height_robust
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --robust -o height_robust_fv
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.mldose \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --robust \
+    -o height_robust
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.dose.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --robust \
+    -o height_robust_fv
 
 diff height_robust_add.out.txt height_robust_fv_add.out.txt
 
+
 echo "Option --robust --interaction=1"
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --robust --interaction=1 -o height_robust_int1
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --robust --interaction=1 -o height_robust_int1_fv
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.mldose \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --robust --interaction=1 \
+    -o height_robust_int1
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.dose.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --robust --interaction=1 \
+    -o height_robust_int1_fv
 
 diff height_robust_int1_add.out.txt height_robust_int1_fv_add.out.txt
 
+
 echo "Option --ngp=2, mlprob file"
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mlprob -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 -o height_ngp2
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.prob.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 -o height_ngp2_fv
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.mlprob \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --ngp=2 \
+    -o height_ngp2
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.prob.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --ngp=2 \
+    -o height_ngp2_fv
 
 diff height_ngp2_add.out.txt height_ngp2_fv_add.out.txt
 diff height_ngp2_domin.out.txt height_ngp2_fv_domin.out.txt
@@ -43,9 +120,22 @@
 diff height_ngp2_recess.out.txt height_ngp2_fv_recess.out.txt
 diff height_ngp2_2df.out.txt height_ngp2_fv_2df.out.txt
 
+
 echo "Option --ngp=2 --allcov"
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mlprob -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --allcov -o height_ngp2_allcov
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.prob.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --allcov -o height_ngp2_allcov_fv
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.mlprob \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --ngp=2 --allcov \
+    -o height_ngp2_allcov
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.prob.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --ngp=2 --allcov \
+    -o height_ngp2_allcov_fv
 
 diff height_ngp2_allcov_add.out.txt height_ngp2_allcov_fv_add.out.txt
 diff height_ngp2_allcov_domin.out.txt height_ngp2_allcov_fv_domin.out.txt
@@ -53,9 +143,22 @@
 diff height_ngp2_allcov_recess.out.txt height_ngp2_allcov_fv_recess.out.txt
 diff height_ngp2_allcov_2df.out.txt height_ngp2_allcov_fv_2df.out.txt
 
+
 echo "Option --ngp=2 --interaction=1"
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mlprob -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --interaction=1 -o height_ngp2_int1
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.prob.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --interaction=1 -o height_ngp2_int1_fv
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.mlprob \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --ngp=2 --interaction=1 \
+    -o height_ngp2_int1
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.prob.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --ngp=2 --interaction=1 \
+    -o height_ngp2_int1_fv
 
 diff height_ngp2_int1_add.out.txt height_ngp2_int1_fv_add.out.txt
 diff height_ngp2_int1_domin.out.txt height_ngp2_int1_fv_domin.out.txt
@@ -63,9 +166,22 @@
 diff height_ngp2_int1_recess.out.txt height_ngp2_int1_fv_recess.out.txt
 diff height_ngp2_int1_2df.out.txt height_ngp2_int1_fv_2df.out.txt
 
+
 echo "Option --ngp=2 --robust"
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mlprob -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --robust -o height_ngp2_robust
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.prob.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --robust -o height_ngp2_robust_fv
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.mlprob \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --ngp=2 --robust \
+    -o height_ngp2_robust
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.prob.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --ngp=2 --robust \
+    -o height_ngp2_robust_fv
 
 diff height_ngp2_robust_add.out.txt height_ngp2_robust_fv_add.out.txt
 diff height_ngp2_robust_domin.out.txt height_ngp2_robust_fv_domin.out.txt
@@ -73,9 +189,22 @@
 diff height_ngp2_robust_recess.out.txt height_ngp2_robust_fv_recess.out.txt
 diff height_ngp2_robust_2df.out.txt height_ngp2_robust_fv_2df.out.txt
 
+
 echo "Option --ngp=2 --robust --interaction=1"
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mlprob -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --robust --interaction=1 -o height_ngp2_robust_int1
-../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.prob.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --robust --interaction=1 -o height_ngp2_robust_int1_fv
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.mlprob \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --ngp=2 --robust --interaction=1 \
+    -o height_ngp2_robust_int1
+../src/palinear \
+    -p ${srcdir}/height.txt \
+    -d ${srcdir}/test.prob.fvi \
+    -i ${srcdir}/test.mlinfo \
+    -m ${srcdir}/test.map \
+    -c 19 --ngp=2 --robust --interaction=1 \
+    -o height_ngp2_robust_int1_fv
 
 diff height_ngp2_robust_int1_add.out.txt height_ngp2_robust_int1_fv_add.out.txt
 diff height_ngp2_robust_int1_domin.out.txt height_ngp2_robust_int1_fv_domin.out.txt